MmuINT0008126 @ mm10
Intron Retention
Gene
ENSMUSG00000041797 | Abca9
Description
ATP-binding cassette, sub-family A (ABC1), member 9 [Source:MGI Symbol;Acc:MGI:2386796]
Coordinates
chr11:110130565-110131874:-
Coord C1 exon
chr11:110131767-110131874
Coord A exon
chr11:110130739-110131766
Coord C2 exon
chr11:110130565-110130738
Length
1028 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGA
5' ss Score
6.91
3' ss Seq
TTGTTTATTATTATTATCAGAAA
3' ss Score
5.29
Exon sequences
Seq C1 exon
GAACACATGCTTTATGAGTACGGATTCATGAGCAACGCATTTTTCTGGATACCAGTGGCTGCCAGCCTCACCCCTTACATTGCGATGGGCAGCATCAGTGACCACAAA
Seq A exon
GTAAGACATTATTAAAGTCTTCAGATCTCCTTCACACCCAGGAAAACTTCCTTTGGATCTTGTGAGCATAGGTAGCGAATCTAATGTGTGTGTTCGTTGCAATATATAATGGAGCATTTCAATAATAGGCTGTCAAAATAGGAATAAAACGCATTTTCCTTAAACAGGATAGCGCCACCAACCAGTAGCAAGTGACAGCTTTTAATTATTCTTGGAGACCACCCTATTCTTCCTACAACACACTCCTTGGTACTCATATCTCATCACAAAGACAGTTTCAACCCAGACCTTTTCCCCGTTTAATAAGGCCCATTAAAAACTGCCATGCAAAATATTTGAATGGGGCTTATGGTCATAAGACTTTCCTCATTTGTTAACTGTTTCTTCTCCACCAGGAATGAATACCACTAAAGTAGCAATGTTTTTTCCTTTAAATTCTGCACATTCTGTTGCTTCCCATCCCAGTGAATAATGGACCGGCCTCTGTTCCCATGCCCTATCAGACACATTTTAAGTGTAAGAGTGTTTGTCTGCATGCATTTATCTATCACATGCATATAGTGCACGTGCCTATGAAGGTTAGGAGAGGATGTCCAGTTCCCTGGAACTAGAGTTACCATCCCTGTTCAAAGTCTCCCTGCACAAGCCTGACAGCTGCCAATCAAGGCATCATGCGCAACAGCTCAGCATTTGTAAATAAAAAATTAAATATAAAAGTGTTTAATAAGGACCTATCGCTAACATCCGTACTCTTGACAGTATCCAGCAGTAGATTAAAAAAAAACCCCTTAGGGAGAGCTGAGTCAACTTATCTGTCTTGTTTTGCAATATTAGCCGTCCCTCTGGTGTAGGGTTGTGGCAAGTGGTGATGTCATTTTCCAAACAAGAGTAATAGTTATTAAAGGGATACAGTAAGAATAGCTGCTGTGACTATGCGTGTGGTTGCCTGGGTCTCAGCTTTCTAGGATTTTATGATGATCTTTATGTTTTGTTTTTGTTTGTTTGTTTTTGTTTATTATTATTATCAG
Seq C2 exon
AAAAAAGTTCTTTCCCAGCTGTGGACTTCAGGCCTTTACCCGTCTGCTTACTGGTGTGGACAGGCTCTGGTGGACATTCCCATATACTTCCTCATTCTCTTTCTCATGCAAATAATGGACAGTGTTTTTAGTTCTGAGGAGTTTATATCTGTGATGGAGAGCCTGTTGATTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041797:ENSMUST00000044850:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF126982=ABC2_membrane_3=FE(11.7=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(19.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAACACATGCTTTATGAGTACGGA
R:
ATCAACAGGCTCTCCATCACAG
Band lengths:
278-1306
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types